A canonical visualization tool for SEEG electrodes

Abstract

Stereoencephalographic (SEEG) electrodes are clinically implanted into the brains of patients with refractory epilepsy to locate foci of seizure onset. They are increasingly used in neurophysiology research to determine focal human brain activity in response to tasks or stimuli. Clear visualization of SEEG electrode location with respect to patient anatomy on magnetic resonance image (MRI) scan is vital to neuroscientific understanding. An intuitive way to accomplish this is to plot brain activity and labels at electrode locations on closest MRI slices along the canonical axial, coronal, and sagittal planes. Therefore, we've developed an open-source software tool in Matlab for visualizing SEEG electrode positions, determined from computed tomography (CT), onto canonical planes of resliced brain MRI. The code and graphical user interface are available at: https://github.com/MultimodalNeuroimagingLab/mnl_seegviewClinical Relevance- This tool enables precise communication of SEEG electrode activity and location by visualization on slices of MRI in canonical axial, coronal, and sagittal planes.

Figure 1.

CT and MRI co-registration. Single-headed arrows represent co-registration of source with target. Double-headed arrow represents cortical segmentation of T1 MRI using FreeSurfer. Electrode positions are obtained from the post-op CT image (CT-post) after co-registration and reslicing. The intermediate co-registration steps involve the T2 MRI and the pre-op CT image (CT-pre) and are recommended for maximum fidelity of alignment. T1 + contrast and FGATIR [5] are examples of ride along images, illustrating how they should be respectively co-registered.

Figure 2.

The SEEG View GUI. The subject’s T1 MRI has been loaded and the anterior commissure is selected (red dot). The brain has not yet been rotated so the three orthogonal views shown do not correspond to the canonical views. The user selects the AC, PC, and three additional points along the mid-sagittal plane to calculate the necessary rotations. Pressing “Launch Reslice” saves the rotated and resliced T1 MRI and ride along images in NIfTI format, along with the transformation matrix necessary to rotate electrodes and brain rendering vertices.

Figure 3.

Brain rendering and canonical slices of the subject’s T1 MRI with SEEG electrodes, depicting results of the face-house visual discrimination task. The canonical slices enable precise anatomic localization of electrodes and reveal house-associated sites deep in the collateral sulcus. (A) 3-D rendering of the subject’s left hemisphere (from FreeSurfer cortical segmentation) with projected SEEG electrodes. Positive electrode weights (red) indicate greater broadband power during house stimuli and negative weights (blue) indicate greater broadband power during face stimuli. (B) Mean log₁₀ power spectral density across all 50 house stimuli (magenta) and all 53 face stimuli (violet), calculated from the representative house-associated site pinpointed in D, E. Frequencies around line noise (60 Hz) and its harmonics (120 Hz, 180 Hz) are omitted. Broadband power is calculated from 70 Hz to 170 Hz (gray rectangle) for each stimulus presentation. (C) Distribution of log₁₀ broadband power for house stimuli (magenta) and face stimuli (violet) at the representative house-associated site. Small black dots depict values for individual stimuli and large black squares depict the mean for all stimuli of each category. (D) Coronal slices of T1 MRI every 8 mm apart with SEEG electrodes plotted each onto the closest slice. The slices span only the volume containing electrodes, as marked by light blue lines in A. Electrode weights are as in A. (E) Axial and sagittal slices of T1 MRI every 8 mm apart with SEEG electrodes plotted. The slices containing the representative house-associated site are shown at the top and framed in their respective montages below.